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Alternative cleavage and polyadenylation: extent, regulation and function
Ran Elkon, Alejandro P.Ugalde and Reuven Agami
Abstract | The 3 end of most protein-coding genes and long non-coding RNAs is cleaved and polyadenylated. Recent discoveries have revealed that a large proportion of these genes contains more than one polyadenylation site. Therefore, alternative polyadenylation (APA) is a widespread phenomenon, generating mRNAs with alternative 3 ends. APA contributes to the complexity of the transcriptome by generating isoforms that differ either in their coding sequence or in their 3 untranslated regions (UTRs), thereby potentially regulating the function, stability, localization and translation efficiency of target RNAs. Here, we review our current understanding of the polyadenylation process and the latest progress in the identification of APA events, mechanisms that regulate poly(A) site selection, and biological processes and diseases resulting from APA.
Photoactivatable
ribonucleoside-enhanced
crosslinking and
immunoprecipitation
(PAR-CLIP). A method for profiling RNA that is bound to a specific protein. Cells are grown in a medium containing 4-thiouridine or 6-thioguanosine, which, when incorporated into RNA, allows for efficient ultraviolet crosslinking to RNA-binding proteins. The immunoprecipitated protein RNA complexes are then used to generate libraries for deep sequencing.
The 3 end of the vast majority of eukaryotic mRNAs contains a long stretch of untemplated adenosines termed the poly(A) tail. Polyadenylation activity was first observed more than 50years ago1. It was recognized as a post-transcriptional modification added to the 3 ends of mRNAs a decade later, and it took yet another decade to unravel the requirement of a dedicated apparatus for processing of 3 ends of mRNAs (recently reviewed in REF.2).
3 end processing is a two-step nuclear process that involves an endonucleolytic cleavage of the transcribed transcript followed by the addition of the poly(A) tail
(FIG.1); this process is required for nuclear export and stability of mature transcripts and for efficient translation of mRNAs3. Intriguingly, poly(A) tails have a restricted length that can greatly differ between species (for example, in humans, some 250300 adenines are added on average compared with 7080 in yeast). The length of poly(A) tails is important, as mRNAs with tails that are too short are, in general, subjected to enzymatic degradation4 or stored in a translationally dormantstate5.
Earlier work identified the canonical cis-acting RNA elements and several dozen...